In the fruit fly, Drosophila melanogaster, accumulation of osk mRNA at the posterior pole of the oocyte and local translation initiate assembly of the pole plasm, which is required for germ cell formation and posterior patterning of the embryo. I have used fluorescence in situ hybridization (FISH) in combination with immunofluorescence and laser scanning confocal microscopy to examine the spatial and temporal control of osk transcript localization and translation. Drosophila oocytes develop within cysts of 16 interconnected cells. One cell in each cyst differentiates to form the oocyte while the remaining cells form nurse cells that produce RNAs and proteins that are transported to the oocyte. osk mRNA is produced by the nurse cells and accumulates in the oocyte throughout oogenesis, but is only specifically localized to the posterior pole and translated during mid to late oogenesis. My studies help define distinct steps in the osk mRNA localization process. An early step in posterior localization is removal of osk mRNA from most of the cortex, leading to accumulation in the oocyte interior. This process requires microtubules, the microtubule motor protein Kinesin I, the actin binding protein Tropomyosin, and the RNA binding protein Staufen. Transcript then moves from the oocyte interior to the posterior pole through a microtubule independent process. The genes cappuccino, chickadee, spire, armitage, maelstrom, par-1 and gurken are all required for this next step in osk mRNA localization. The final capturing or tethering osk mRNA at the cortex requires an intact actin filament system, but additional components of this anchoring system remain to be identified. I also find that osk mRNA first begins to accumulate at the posterior pole during oogenesis stage 8, but protein is not detectable until stage 9. In addition, grk and par-1 mutations that block osk mRNA localization to the posterior pole and lead to transcript accumulation in the interior do not prevent translation; again, Osk protein production is only observed during stage 9 and later. These observations indicate that posterior localization is neither sufficient nor necessary to trigger osk mRNA translation, which appears to be under tight temporal control.

O constante aumento da velocidade de processamento, devido principalmente à utilização de um número cada vez maior de processadores, tem propiciado grandes avanços no projeto e na construção de sistemas computacionais paralelos. Entretanto o desempenho de muitas aplicações é afetado pela latência das operações de Entrada e Saída de dados. Para solucionar esse problema, sistemas de arquivos paralelos, que oferecem acesso paralelo aos dados armazenados em diversos discos, vêm sendo desenvolvidos. O desenvolvimento desses sistemas complexos pode ser beneficiado pela adoção de Técnicas de Descrição Formal (TDFs), durante as fases de projeto e especificação dos mesmos, as quais podem ser aliadas a técnicas de implementação durante as demais fases. Neste sentido, este projeto propõe uma abordagem baseada em frameworks e na TDF Extended State Transition Language (Estelle), para a especificação formal, validação, implementação e teste de sistemas dessa categoria. Um framework conceitual que descreve um sistema funcional é apresentado, e dois estudos de caso são desenvolvidos dando origem a dois sistemas de arquivos derivados do framework. Uma metodologia para a validação, que usa ferramentas de simulação, é apresentada. Um dos estudos de caso é implementado semi-automaticamente, a partir de sua especificação formal Estelle, e comparações de desempenho com o mesmo sistema implementado manualmente são realizadas. / The constant increase of processing speed, mainly due to the use of a large number of processors, has allowed an improvement in the design and building of parallel computation systems. However, the performance of several types of applications is affected by the latency originated from Input/Output operations on data. In order to solve this problem parallel file systems, which allow parallel access to the data stored on a set of discs, have been developed. The design of such complex systems can benefit from the adoption of implementation techniques allied with Formal Description Techniques (FDTs). Aimed to introduce the use of FDTs in the development cycle of distributed parallel file systems, this work proposes an approach, based on framework and the FDT Extended State Transition Language (Estelle), for the formal specification, validation, implementation and testing of systems belonging to this domain. A conceptual framework that describes a basic functional system is presented, and two case studies are developed from it. A methodology for Estelle specification validation that makes use of simulation tools is also proposed in this work. One of the systems, developed as a case study, is semi-automatically implemented from its Estelle formal specification, and performance comparisons with a hand-coded implementation of the same system are done.

A specification of a software program, hardware component, or system, is a description of what the system is required to do without describing how it is to be done. Specifications provide the necessary details for system developers, suppliers, users and regulators to understand and agree upon the requirements of a system. It is therefore vital that specifications are clear, concise, complete, and are free of ambiguity and inconsistency. Specifications are usually expressed using a combination of informal natural language descriptions, diagrams, and formal mathematical techniques. The degree to which formal mathematics is used depends on the nature of the application and the criticality of the function being described. In industries where the cost of a system or software failure is high, such as national defence and government, banking, transport, energy, and communication, and some manufacturing industries, formal specification is recommended because it offers greater clarity and consistency, and moreover, formal specification are machine readable, allowing some automated checking to be applied. However, poorly written formal specifications can be less useful than informal specifications if they are unreadable (or not clear), or if they are overly large or complex (or not concise), making it hard to determine whether they are consistent or complete. In particular, if the system itself is large or complex, or it features multiple and diverse aspects of behaviour, it can be difficult to capture all aspects of its behaviour clearly and concisely in a monolithic formal model, or within a single formal notation. In many cases this is because the modeling approach may be particularly suited to some aspects of the system but not to others. The widely accepted solution to this problem is to use diverse modeling techniques to specify the different aspects of the system from different viewpoints. This results in a number of view specifications that taken together make up the complete specification of the system. The thesis introduces structuring mechanisms for the formal specification language Z that allow the view specifications of a system to be described, combined and reused. Specification encapsulation and parameter abstraction and application are explored along with object-oriented concepts such sub-typing and sub-classing. Two case studies, which are based on a language-based editor and a database system, are provided to illustrate how the techniques developed in this thesis may be used.

<p>Two new specification tests for overidentifying restrictions proposed by Hahn and Hausman (2002:b) are here tested and compared to the classical Sargan test. Power properties are found to be very similar in overall performance, while Sargan generally has better size than the new tests. Also, size is distorted for one of the new tests, thus a tendency to reject prevails. In addition, sometimes severe bias is found which affects the tests’ performances, something that differs from earlier studies.</p>

Requirements acquisition is one of the most important and least well supported parts of the software development process. The Requirements Apprentice (RA) will assist a human analyst in the creation and modification of software requirements. Unlike current requirements analysis tools, which assume a formal description language, the focus of the RA is on the boundary between informal and formal specifications. The RA is intended to support the earliest phases of creating a requirement, in which incompleteness, ambiguity, and contradiction are inevitable features. From an artificial intelligence perspective, the central problem the RA faces is one of knowledge acquisition. It has to develop a coherent internal representation from an initial set of disorganized statements. To do so, the RA will rely on a variety of techniques, including dependency-directed reasoning, hybrid knowledge representation, and the reuse of common forms (clich鳩. The Requirements Apprentice is being developed in the context of the Programmer's Apprentice project, whose overall goal is the creation of an intelligent assistant for all aspects of software development.

No description available.

Pluripotent stem cells have the capacity to develop into different cell lineages and can be manipulated into certain cell types through the use of small molecule inducers. Retinoic acid (RA) signaling through retinoic acid receptors (RAR) and retinoid X receptors (RXR) has the ability to direct lineage determination but has yielded disappointing results in promoting skeletal myogenesis in embryonic stem (ES) cells. RXR is crucial in embryonic development although it is generally considered to act as a silent partner for other nuclear receptors such as RAR. Our findings demonstrate that rexinoid specific signaling enhances skeletal myogenesis and requires β-catenin but not RAR. Moreover, RXR signalling in mouse ES cells can efficiently enhance skeletal myogenesis and closely recapitulates sequential events observed in vivo. Since ES cells closely represent the properties of the developing embryo, efficiently generating skeletal muscle provides a means to further scrutinize signaling pathways in myogenic development in view of developing therapies for muscle related diseases.

The Unified Modeling Language (UML) is widely used by software engineers as the basis of analysis and design in software development. However, UML ignores human factors in the course of software development because of its strong emphasis on the internal structure and functionality of the application. This thesis presents a method of mapping human-computer interaction (HCI) requirement specifications generated by usability engineering (UE) methodologies (e.g. Putting Usability First (PUF)) into UML specifications. These two sets of requirement specification are specified, using Extensible Markup Language (XML) so that HCI requirement specifications can be integrated into UML ones. A Mapping Tool was developed to facilitate the creation of mappings between PUF XML tags and XMI tags. The Mapping Tool was used to create mappings between PUF and UML requirement specifications. This mapping process and its outputs were evaluated to demonstrate that the tool worked. The results of the evaluation show that the HCI requirement specification represented by the PUF XML tags can improve the UML specification by adding them into the XMI tags.

Although numerous transcription factors (TFs) are expressed by oligodendrocytes (OGs), the role(s) of most of these TFs in oligodendrogenesis remains to be elucidated. One such TF is Hoxa2, which was recently shown to be expressed by O4-positive (+) pro-OGs. Hence, the main objectives of this thesis were to determine the expression profile and function(s) of Hoxa2 during OG development. Immunocytochemical analysis of primary mixed glial cultures demonstrated that Hoxa2 is expressed throughout oligodendrogenesis, diminishing only with the acquisition of a myelinating phenotype. Subsequently, immunohistochemical analysis suggested that Hoxa2 is expressed by migratory oligodendroglial cells in the embryonic spinal cord. However, double immunofluorescent analysis of Hoxa2 transgenic knockout mice showed that OG specification and early maturation proceed normally in the absence of Hoxa2 in the spinal cord. As Hoxa2 is one of 39 murine Hox genes, which exhibit extensive overlapping expression profiles in the spinal cord, we decided to examine the expression of an additional Hox TF, Hoxb4, during OG development. Immunocytochemical analysis of primary mixed glial cultures demonstrated that Hoxb4 is also expressed throughout OG development. Furthermore, comparison of the expression profiles of Hoxb4 and Olig2 suggested that Hoxb4 is expressed by oligodendroglial cells in the spinal cord. Hence, Hoxb4, as well as other Hox TFs could compensate for Hoxa2 in the spinal cord in its absence. As the anterior boundary of most Hox genes has been found to be in the hindbrain or spinal cord, we decided to look at the telencephalon which would be less likely to have compensatory mechanisms. Our results showed that similar to the spinal cord, Hoxa2 is expressed by oligodendroglial cells in the telencephalon. Subsequently, it was found that over-expressing Hoxa2 in CG4 cells, an oligodendroglial cell line derived from the perinatal rat cerebral cortex, impairs their differentiation. In an attempt to determine the mechanism by which it accomplishes this, we examined the expression of polysialylated neural cell adhesion molecule (PSA-NCAM), which has been implicated in this process. Contrary to our expectations, however, it was found that over-expressing Hoxa2 in CG4 cells results in significantly fewer PSA-NCAM+ cells. Hence, the results suggest that Hoxa2s effect on OG differentiation is independent of its effect on PSA-NCAM expression. The expression of Hox genes is enhanced by retinoic acid (RA), which, in turn, both inhibits, as well as promotes OG differentiation. Although the reason for these opposing roles is uncertain, examination of the experimental protocols utilized by different research groups reveals disparities in age, CNS region, as well as RA concentration. As a result, RAs effect on oligodendrogenesis could be stage- and/or concentration-dependent. In order to determine which of these factors could impact RAs effect on OG differentiation we treated CG4 cells with two different concentrations of RA at two distinct time points. The results showed that both factors (concentration and time/stage) can impact RAs effect on CG4 cell differentiation. In an attempt to determine the mechanism by which it accomplishes this, we examined the expression of PSA-NCAM. Contrary to our expectations, the results suggest that RAs effect on CG4 differentiation is independent of its effect on PSA-NCAM expression. The results of this thesis suggest that Hoxa2 and RA could play multiple roles in OG development. Although these roles appear to be similar, further research will be needed to determine whether Hoxa2 acts a downstream effector in the RA signaling pathway in oligodendroglial cells.

Orchestrated web service applications are highly distributed applications that accomplish business goals by executing services offered by partners. This dependance on partner services allows the development of more flexible, modular applications. For a classical distributed system, correctness can be ensured by statically checking the composition of the components that make up the system against properties of interest. However, in the case of web service applications, there are various conditions that make this type of analysis insufficient. For example, partners can be dynamically discovered, which means that we cannot create a definitive model of the system to analyze. Web service applications can also display new behaviour at execution time, so statically checked properties of the system may not hold throughout the system's lifetime. Due to these limitations of static analysis, this thesis concentrates on the dynamic analysis of web service applications, specifically, by monitoring runtime events. The goal of runtime monitoring is to check whether an application violates a given specification of its behaviour during its execution. The behaviour of the system can be specified in a number of ways, e.g., as a set of temporal properties, assertions or even scenarios. During execution, application events are intercepted and used to determine if the system is violating its specification. Moreover, monitoring the system as it runs provides a chance to recover from an error once a problem has been detected. This is critical in the domain of web service applications, as bugs are potentially exposed to millions of users before they are found/fixed. We present techniques to address several major challenges facing the creation of an industrial-strength runtime monitoring and recovery framework for web service applications. The first milestone for achieving this goal is the creation of an adequate property specification language. This language must be expressive enough to capture the distributed, interactive, and message-driven nature of web service applications, but must also be amenable to efficient runtime monitoring. We propose Web Sequence Diagrams (W-SD), a language that, we feel, meets these criteria. Specifications expressed in W-SD permit the analysis of orchestrations involving multiple partners, from the point of view of the orchestrating service. The second contribution of this thesis is the creation of an industrial-strength online runtime monitoring and recovery framework that is non-intrusive, supports the dynamic discovery of web services, deals with synchronous and asynchronous communication, as well as partner services implemented in different languages. Developers using this framework can specify and efficiently monitor a variety of temporal behaviour. If recovery is enabled, properties are monitored proactively, so this framework allows developers to effortlessly enable error recovery in applications being monitored. The last contribution of this thesis is the development of recovery plans from runtime errors. Given an application path which led to a failure and a monitor which detected it, we have developed various techniques and optimizations that make recovery plan generation feasible in practice. For some of the violations, such plans essentially involve "going back" -- compensating the occurred actions until an alternative behaviour of the application is possible. For other violations, such plans include both "going back" and "re-planning" -- guiding the application towards a desired behaviour.